Authors:Savannah Gleim; Stuart J. SmythPages: 26 - 32Abstract: Publication date: 25 May 2018 Source:New Biotechnology, Volume 42 Author(s): Savannah Gleim, Stuart J. Smyth Part of what is presently missing at domestic regulatory levels (and that is important at the international level as well) is a detailed understanding of what the rules of, and for, regulation should be, who the actors, stakeholders and major decision makers are and finally, how to get agreement about the rules. Greater insights into the system of rules that underpin regulatory frameworks for agri-food and biotechnology products in genetically modified (GM) crop- adopting nations will provide value by clarifying the evidence used to commercialize these technologies. This article examines the public documents available from Canada, the United States, the European Union and the Organisation for Economic Cooperation and Development regarding the development of regulatory risk assessment frameworks for products of biotechnology to determine what science grounds these frameworks. The documentation used to provide the initial structure to the existing regulatory frameworks identifies the linkages, connections and relationships that exist between science, risk assessment and regulatory policy. The relationship between risk and regulation has never been more critical to the commercialization of innovative agricultural products. Documenting the role of science-based risk assessment in regulations and how this has changed over the 20 years of experience in regulating GM crops will identify changes in the risk/regulation relationship.

Authors:Edouard I.R. Sanou; Godelieve Gheysen; Bazoumana Koulibaly; Caspar Roelofs; Stijn SpeelmanPages: 33 - 41Abstract: Publication date: 25 May 2018 Source:New Biotechnology, Volume 42 Author(s): Edouard I.R. Sanou, Godelieve Gheysen, Bazoumana Koulibaly, Caspar Roelofs, Stijn Speelman In 2008, the commercial cultivation of Genetically Modified (GM) cotton (Bollgard II®) started in Burkina Faso. The adoption rate increased rapidly in subsequent years to reach around 70% in 2014. Although some criticisms were raised concerning the suitability of the technology for the farming system in Burkina Faso, the introduction of transgenic cotton in the country was generally regarded as a great success. Despite this, during the 2016–2017 agricultural campaign, the government of Burkina Faso decided to suspend the cultivation of Bollgard II®. In this context, this paper investigates farmers’ knowledge, perceptions, opinions and attitudes towards Bollgard II® as well as their views on the recent decision to suspend its cultivation. Data was collected from 324 cotton farmers, both growers of conventional and Bollgard II®. The results showed that the farmers surveyed had a poor knowledge concerning the core concepts of biotechnology and Bollgard II® in particular. Moreover, the regulatory oversight of the implementation of the technology was found insufficient, as illustrated by the lack of compliance with prescriptions concerning refuge areas and pesticide treatments. Nevertheless, overall, the farmers interviewed had a slightly positive opinion about the effects on yield, income and their wellbeing. In particular the reduction in pesticide treatments was perceived very positively by all respondents. Although the study finds that the majority of farmers disagreed with the recent suspension of Bt cotton cultivation by the government, it also makes clear that a thorough debate on the technology and its implementation is necessary.

Authors:Greet Smets; Patrick RüdelsheimPages: 42 - 47Abstract: Publication date: 25 May 2018 Source:New Biotechnology, Volume 42 Author(s): Greet Smets, Patrick Rüdelsheim Conventionally, chitosans are derived from shrimp and other crustacean shells. Biotechnology offers an alternative route to produce chitosans and more importantly, specific chitosan structures tailored to the needs of a diversity of industries. However, for biotech chitosans and products thereof to be commercialised, legislation should not create a burden. Here, the requirements of the EU regulatory framework have been analysed for the entire chain from research to development and production of several potential applications including nanomaterials. The animal or biotechnological origin leads to specific requirements in production of the raw material. No EU legislation dedicated to nanomaterials has been adopted. Instead, products are governed under the respective existing product legislation subject to extra requirements for safety assessment. While a knowledge gap exists on hazards related to nanomaterials in general, there is a need to establish realistic regulatory study designs to assess the safety of specific products. Furthermore, as many of the existing chitosan applications are not considered nanomaterials, it would be discriminatory to treat biotechnology derived products differently.

Authors:Karolina Chreptowicz; Jolanta MierzejewskaPages: 56 - 61Abstract: Publication date: 25 May 2018 Source:New Biotechnology, Volume 42 Author(s): Karolina Chreptowicz, Jolanta Mierzejewska Increasing demand for natural fragrance ingredients and products has led to their global market growth. 2-Phenylethanol (2-PE) is a volatile substance widely used in food and cosmetics manufacturing. It is generally known that yeast can metabolize l-phenylalanine (l-Phe) to produce 2-PE. However, because the product exhibits an inhibitory effect on yeast cells, simple batch cultivation is uneconomic. The aim of this study was to enhance 2-PE productivity using in situ product removal. Here we present a new method of 2-PE production by yeast in a biphasic system with rapeseed oil as the second phase. The chosen solvent is safe, inexpensive and suitable for the extraction of 2-PE. In addition, rapeseed oil appeared to be a valuable source of intermediates for 2-PE synthesis as its presence in the yeast culture significantly enhanced productivity. The process is an environmentally friendly route and gives two final products that can be considered natural: rapeseed oil with a rose odor and pure 2-PE. Both may be subsequently used as food or cosmetics additives. The results obtained are competitive with previously reported values, as it was possible to enhance the overall concentration of 2-PE by 2.7-fold. The total 2-PE concentration in the biphasic system in the 4.5-L biofermentor used was increased to 9.79 g/L, while the 2-PE concentration in the organic phase attained a value of 18.50 g/L. Graphical abstract

Authors:Jim PhilpPages: 11 - 19Abstract: Publication date: 25 January 2018 Source:New Biotechnology, Volume 40, Part A Author(s): Jim Philp During the Industrial Revolution, it became clear that wood was unsuited as an energy source for industrial production, especially iron smelting. However, the transition to coal was the effort of decades. Similarly, the transition from coal to oil was neither a smooth nor rapid process. The transition to an energy and materials production regime based on renewable resources can similarly be expected to be fraught with many setbacks and obstacles, technically and politically. Those earlier transitions, however, were not complicated by the so-called grand challenges faced today. Above energy security and food and water security lurks climate change. Some events of 2015 have politically legitimised climate change and its mitigation, and 2016 saw the world finally sworn to action. The bioeconomy holds some of the answers to the economic challenges thrown up by mitigating climate change while maintaining growth and societal wellbeing. For bioeconomy policy makers, the future is complex and multi-faceted. The issues start in regions and extend to global reach. It is hard to quantify what is going to be the most difficult of challenges. However, one of the visions for the bioeconomy, that of distributed manufacturing in small- and medium-scale integrated biorefineries flies in the face of the current reality of massive fossil fuel and petrochemical economies of scale, married to gargantuan fossil fuel consumption subsidies.

Authors:Christian Patermann; Alfredo AguilarPages: 20 - 24Abstract: Publication date: 25 January 2018 Source:New Biotechnology, Volume 40, Part A Author(s): Christian Patermann, Alfredo Aguilar This article outlines the context and circumstances that favoured the development of a Bioeconomy Strategy in the European Union (EU) and the role played by the different Framework programmes for Research, Technological Development and Demonstration. Particular attention is given to the biotechnology related programmes and more specifically to the “Cell Factory” Key Action in the 5th Framework Programme (1998–2002). This, together with the parallel development of a Strategy on Biotechnology in 2002, served as a solid foundation for the creation of the, at the time, so-called Knowledge-Based Bio-Economy (KBBE). The KBBE concept emerged in 2005, a couple of years before the launch of the 7th Framework Programme (2007–2013). The experience accumulated over the years and the new societal expectations triggered the EU to launch a Strategy on Bioeconomy in 2012. This article concludes with a brief analysis of the two most important impacts of the EU Strategy on Bioeconomy. One is the Bioeconomy dedicated activity within the Programme Horizon 2020 (2014–2020), and the other the creation of a public-private partnership of bio-based industries. Both the impact of Horizon 2020 on the EU Bioeconomy Strategy and the bio-based industries public-private partnership are analysed in depth in two articles elsewhere in this volume.

Authors:Philippe Mengal; Marcel Wubbolts; Eleni Zika; Ana Ruiz; Dieter Brigitta; Agata Pieniadz; Sarah BlackPages: 31 - 39Abstract: Publication date: 25 January 2018 Source:New Biotechnology, Volume 40, Part A Author(s): Philippe Mengal, Marcel Wubbolts, Eleni Zika, Ana Ruiz, Dieter Brigitta, Agata Pieniadz, Sarah Black This article discusses the preparation, structure and objectives of the Bio-based Industries Joint Undertaking (BBI JU). BBI JU is a public-private partnership (PPP) between the European Commission (EC) and the Bio-based Industries Consortium (BIC), the industry-led private not-for-profit organisation representing the private sectors across the bio-based industries. The model of the public-private partnership has been successful as a new approach to supporting research and innovation and de-risking investment in Europe. The BBI JU became a reality in 2014 and represents the largest industrial and economic cooperation endeavour financially ever undertaken in Europe in the area of industrial biotechnologies. It is considered to be one of the most forward-looking initiatives under Horizon 2020 and demonstrates the circular economy in action. The BBI JU will be the catalyst for this strategy to mobilise actors across Europe including large industry, small and medium-sized enterprises (SMEs), all types of research organisations, networks and universities. It will support regions and in doing so, the European Union Member States and associated countries in the implementation of their bioeconomy strategies.

Authors:Ana C. Fernandes; Daria Semenova; Peter Panjan; Adama M. Sesay; Krist V. Gernaey; Ulrich KrühneAbstract: Publication date: Available online 6 March 2018 Source:New Biotechnology Author(s): Ana C. Fernandes, Daria Semenova, Peter Panjan, Adama M. Sesay, Krist V. Gernaey, Ulrich Krühne The limited availability of metabolite-specific sensors for continuous sampling and monitoring is one of the main bottlenecks contributing to failures in bioprocess development. Furthermore, only a limited number of approaches exist to connect currently available measurement systems with high throughput reactor units. This is especially relevant in the biocatalyst screening and characterization stage of process development. In this work, a strategy for sensor integration in microfluidic platforms is demonstrated, to address the need for rapid, cost-effective and high-throughput screening in bioprocesses. This platform is compatible with different sensor formats by enabling their replacement and was built in order to be highly flexible and therefore suitable for a wide range of applications. Moreover, this re-usable platform can easily be connected to analytical equipment, such as HPLC, lab scale reactors or other microfluidic chips through the use of standardized fittings. Also, the developed platform includes a two-sensor system interspersed with a mixing channel, which allows the detection of samples that might be outside the first sensor’s range of detection, through dilution of the sample solution up to 10 times. In order to highlight the features of the proposed platform, inline monitoring of glucose levels is presented and discussed. Glucose was chosen due to its importance in biotechnology as a relevant substrate. The platform demonstrated continuous measurement of substrate solutions for up to 12 h. Furthermore, the influence of the fluid velocity on substrate diffusion was observed, indicating the need for in-flow calibration to achieve a good quantitative output.

Authors:Saša Vrhovec Hartman; Bojan Božič; Jure DergancAbstract: Publication date: Available online 6 March 2018 Source:New Biotechnology Author(s): Saša Vrhovec Hartman, Bojan Božič, Jure Derganc Microcavities provide a well-controlled flow-free microenvironment and play an important role in many microfluidic systems, for example as cell-culturing microchambers. Here we show that transient concentration gradients that emerge during diffusive exchange of solutes in microcavities induce passive migration (diffusiophoresis) of blood cells and synthetic phospholipid vesicles. The passive migration is observed in various concentration gradients comprising non-electrolytes and electrolytes, i.e., glucose, sucrose, sodium chloride, potassium chloride, potassium benzoate, and potassium sulfate. The results complement prior reports, where gradients of non-electrolytes and monovalent salts, produced by micropipette injection, did not induce a noticeable migration of vesicles. The migration distances measured depended on the solution and the cell or vesicle type, and were in the range of several tens of micrometers. The results show that diffusiophoresis of cells and vesicles is a notable phenomenon in a flow-free environment and has to be taken into account when an accurate spatiotemporal control of cells or vesicles in microcavities is required. Graphical abstract

Authors:Kohei Seta; Toshihiro Suzuki; Keiji Kiyoshi; Toshiya Shigeno; Toshiaki Nakajima-KambeAbstract: Publication date: Available online 26 February 2018 Source:New Biotechnology Author(s): Kohei Seta, Toshihiro Suzuki, Keiji Kiyoshi, Toshiya Shigeno, Toshiaki Nakajima-Kambe A methane fermentation digested slurry (MFDS) was evaluated as a substitute for the commercial nutrient, yeast extract (YE), in ethanol production from glycerol by Klebsiella variicola strain TB-83D. In pH-controlled fed-batch cultures, partial replacement of YE by MFDS did not reduce ethanol productivity significantly. However, non-sterilized MFDS had negative effects on glycerol fermentation by this strain. Although ethanol production decreased when YE was completely replaced by sterilized MFDS, the use of crude glycerol and sterilized MFDS achieved a yield of 14.6 g/L ethanol. This is the first study to report the use of MFDS as the sole nutrient for ethanol production from glycerol, which contributes to the development of a low-cost glycerol biorefinery derived from the biodiesel fuel industry.

Authors:Stefania De Giorgi; Noura Raddadi; Angelo Fabbri; Tullia Gallina Toschi; Fabio FavaAbstract: Publication date: Available online 21 February 2018 Source:New Biotechnology Author(s): Stefania De Giorgi, Noura Raddadi, Angelo Fabbri, Tullia Gallina Toschi, Fabio Fava Lactobionic acid (LBA) is a fine chemical largely applied in the food, chemical, cosmetics and pharmaceutical industries. Here, its production from ricotta cheese whey (RCW), or scotta, the main by-product obtained from ricotta cheese production process and currently employed mainly for cattle feed, was evaluated. Among seven bacterial species tested, only two Pseudomonas taetrolens strains were selected after preliminary screening in shake-flasks. When autoclaved RCW was used, a lactobionic acid titer of 34.25 ± 2.86 g/l, with a conversion yield (defined as mol LBA/mol of consumed lactose %) of up to 85 ± 7.0%, was obtained after 48 h of batch fermentation in 3 L stirred tank bioreactor. This study is a preliminary investigation on the potential industrial use of scotta as a substrate for bacterial growth and lactobionic acid production that details the possible biotechnological valorization pathways and feasibility of the process.

Authors:Kalpana Nautiyal; Yutaka KurodaAbstract: Publication date: Available online 12 February 2018 Source:New Biotechnology Author(s): Kalpana Nautiyal, Yutaka Kuroda Tobacco Etch Virus (TEV) protease is used in the purification of recombinant proteins, but its use is often hampered by solubility issues. Here, we report a short, 12-residue solubility enhancing peptide (SEP) tag attached at the C-terminus of TEV (TEV-C9R). We assessed the effects of the C9R tag on the biophysical and biochemical characteristics of TEV. The yield of HPLC purified TEV-C9R expressed in E. coli grown in 200 mL LB or TB media was between 10 and 13 mg, which was up to 6.5 times higher than the yield of the untagged TEV. TEV-C9R was active over a pH range of 5–8, which was wider than that of the commonly used thrombin, and it remained active upon incubation at 60 °C much longer than the untagged TEV, which aggregated at this temperature. Static and dynamic light scattering demonstrated the higher solubility of purified TEV-C9R. Furthermore, the thermal unfolding of TEV-C9R, as assessed by circular dichroism at pH 4.7, was almost perfectly reversible, in contrast to that of untagged TEV, which aggregated at high temperature. These results demonstrate the improved biophysical and biochemical characteristics of TEV-C9R originating from higher solubility and provide another example of how SEP tags can enhance enzyme solubility without altering its activity.

Authors:Daniel Grajales; Juan Carlos Mateos; Daniel Padro; Pedro Ramos-Cabrer; Fernando López-GallegoAbstract: Publication date: Available online 10 February 2018 Source:New Biotechnology Author(s): Daniel Grajales, Juan Carlos Mateos, Daniel Padro, Pedro Ramos-Cabrer, Fernando López-Gallego Protein immobilization is a key enabling technology for flow biocatalysis. For this purpose, many different immobilization protocols and characterization techniques have been developed in recent decades. However, examples where proteins are directly immobilized on ready-to-use reactors are scarce, likely due to the lack of analytical tools to monitor in-flow protein immobilization in a non-invasive manner. Here, we have for the first time exploited Magnetic Resonance Imaging (MRI) to characterize in-flow protein immobilization on pre-packed bed columns. This concept was demonstrated by in-flow immobilization of a green fluorescence protein. MRI analysis revealed that both the protein concentration of the flushed solution and flow rate play key roles in controlling the spatial organization of the protein across the packed-bed reactor. This analytical tool coupled to in-flow protein immobilization has been expanded to more industrially relevant enzymes, such as the lipase from Thermomyces lanuginosus, achieving a ready-to-use reactor packed with a heterogeneous biocatalyst with high activity (up to 3000 U x g-1) and high stability (75% residual activity after 1 h incubation at 60 °C). Introducing new analytical tools during the fabrication of heterogeneous biocatalysts will contribute to make the process of immobilizing proteins on solid carriers more rational than currently is. Graphical abstract

Authors:Nika Schwartz; Michal Pellach; Yair Glick; Reuven Gil; Gahl Levy; Dorit Avrahami; Efrat Barbiro-Michaely; Yaakov Nahmias; Doron GerberAbstract: Publication date: Available online 10 February 2018 Source:New Biotechnology Author(s): Nika Schwartz, Michal Pellach, Yair Glick, Reuven Gil, Gahl Levy, Dorit Avrahami, Efrat Barbiro-Michaely, Yaakov Nahmias, Doron Gerber The hepatitis C virus (HCV) non-structural protein 3 (NS3) is essential for HCV maturation. The NS3/4A protease is a target for several HCV treatments and is a well-known target for HCV drug discovery. The protein is membrane associated and thus probably interacts with other membrane proteins. However, the vast majority of known NS3 host partners are soluble proteins rather than membrane proteins, most likely due to lack of appropriate platforms for their discovery. Utilization of an integrated microfluidics platform enables analysis of membrane proteins in their native form. We screened over 2800 membrane proteins for interaction with NS3 and 90 previously unknown interactions were identified. Of these, several proteins were selected for validation by co-immunoprecipitation and for NS3 proteolytic activity. Bearing in mind the considerable number of interactions formed, together with the popularity of NS3/4A protease as a drug target, it was striking to note its lack of proteolytic activity. Only a single protein, Neuregulin1, was observed to be cleaved, adding to the 3 known NS3/4A cleavage targets. Neuregulin1 participates in neural proliferation. Recent studies have shown its involvement in HCV infection and hepatocellular carcinoma. We showed that NS3/4A triggers an increase in neuregulin1 mRNA levels in HCV infected cells. Despite this increase, its protein concentration is decreased due to proteolytic cleavage. Additionally, its EGF-like domain levels were increased, possibly explaining the ErbB2 and EGFR upregulation in HCV infected cells. The newly discovered protein interactions may provide insights into HCV infection mechanisms and potentially provide new therapeutic targets against HCV.

Authors:Domenico Andrea Cristaldi; Fatih Yanar; Ali Mosayyebi; Pablo García-Manrique; Eugen Stulz; Dario Carugo; Xunli ZhangAbstract: Publication date: Available online 6 February 2018 Source:New Biotechnology Author(s): Domenico Andrea Cristaldi, Fatih Yanar, Ali Mosayyebi, Pablo García-Manrique, Eugen Stulz, Dario Carugo, Xunli Zhang The translation of continuous-flow microreactor technology to the industrial environment has been limited by cost and complexity of the fabrication procedures and the requirement for specialised infrastructure. In the present study, we have developed a significantly cost-effective and easy-to-perform fabrication method for the generation of optically transparent, continuous-flow reactors. The method combines 3D printing of master moulds with sealing of the PDMS channels’ replica using a pressure-sensitive adhesive tape. Morphological characterisation of the 3D printed moulds was performed and reactors were fabricated with an approximately square-shaped cross-section of 1 mm2. Notably, they were tested for operation over a wide range of volumetric flow rates, up to 20 ml/min. Moreover, the fabrication time (i.e., from design to the finished product) was <1 day, at an average material cost of ∼£5. The flow reactors have been applied to the production of both inorganic nanoparticles (silver nanospheres) and organic vesicular systems (liposomes), and their performance compared with reactors produced using more expensive and laborious fabrication methods Numerical simulations were performed to characterise the transport of fluids and chemical species within the devices. The developed fabrication method is suitable for scaled-up fabrication of continuous-flow reactors, with potential for application in biotechnology and nanomedicine. Graphical abstract

Authors:Anita Šalić; Ana Jurinjak Tušek; Aleksandra Sander; Bruno ZelićAbstract: Publication date: Available online 5 February 2018 Source:New Biotechnology Author(s): Anita Šalić, Ana Jurinjak Tušek, Aleksandra Sander, Bruno Zelić Although the application of microreactors in different processes has been extensively explored in recent decades, microreactors continue to be underexplored in the context of the enzyme-catalysed process for biodiesel production. Due to their numerous advantages, microreactors could become the next step in the development of a biodiesel production process characterised by sustainability, cost-effectiveness and energy efficiency. In this investigation, biodiesel production was catalysed by lipase from Thermomyces lanuginosus (Lipolase L100). Edible sunflower oil was used as a model substrate in order to investigate the process. After optimal process conditions had been determined, waste-cooking oil was used for biodiesel production to make the production process more sustainable. Three different substrate-feeding strategies were investigated and finally an optimal strategy was proposed. In all the investigated systems, fatty acids methyl esters (FAME) content was higher than 95% and obtained in a significantly shorter time (less than 2 h) compared to the batch process in which biodiesel production was catalysed by lipase (C = 95%, t = 96 h). After the optimal biodiesel production system had been proposed, an integrated system with two microchips connected in series was developed. The first microchip was used for biodiesel production and the second for simultaneous purification i.e. glycerol separation. Finally, purified biodiesel was produced with glycerol content below the detection limit.

Authors:Simon. L. GoodmanAbstract: Publication date: Available online 3 February 2018 Source:New Biotechnology Author(s): Simon. L. Goodman The biological literature reverberates with the inadequacies of commercial research-tool antibodies. The scientific community spends some $2 billion per year on such reagents. Excellent accessible scientific platforms exist for reliably making, validating and using antibodies, yet the laboratory end-user reality is somehow depressing – because they often “don’t work”. This experience is due to a bizarre and variegated spectrum of causes including: inadequately identified antibodies; inappropriate user and supplier validation; poor user training; and overloaded publishers. Colourful as this may appear, the outcomes for the community are uniformly grim, including badly damaged scientific careers, wasted public funding, and contaminated literature. As antibodies are amongst the most important of everyday reagents in cell biology and biochemistry, I have tried here to gently suggest a few possible solutions, including: a move towards using recombinant antibodies; obligatory unique identification of antibodies, their immunogens, and their producers; centralized international banking of standard antibodies and their ligands; routine, accessible open-source documentation of user experience with antibodies; and antibody-user certification.

Authors:Daniela Huber; Klaus Bleymaier; Alessandro Pellis; Robert Vielnascher; Andreas Daxbacher; Katrin J. Greimel; Georg M. GuebitzAbstract: Publication date: Available online 6 January 2018 Source:New Biotechnology Author(s): Daniela Huber, Klaus Bleymaier, Alessandro Pellis, Robert Vielnascher, Andreas Daxbacher, Katrin J. Greimel, Georg M. Guebitz Pharmaceuticals contaminate the environment for several reasons, including metabolic excretion after intake, industrial waste and improper disposal. The narcotic drug morphine is commonly utilized for chronic pain management, and the distribution of morphine in aqueous systems and in waste waters is of high concern. Here. the removal of morphine by a laccase from Myceliophthora thermophila both in its free form as well as immobilized on Accurel MP1000 beads was investigated. Complete morphine elimination was achieved within 30 min for the free and the immobilized enzyme (70% bound protein) for concentrations between 1 and 1,000 mg L−1 according to LC-TOF mass spectrometry analysis. Higher morphine concentrations up to 60 g L−1 were also tested and total elimination was achieved within 6 h. Therefore, laccases are ideal candidates for removing morphine from aqueous systems.

Authors:Dulce María Arias; Enrica Uggetti; María Jesús García-Galán; Joan GarcíaAbstract: Publication date: Available online 3 January 2018 Source:New Biotechnology Author(s): Dulce María Arias, Enrica Uggetti, María Jesús García-Galán, Joan García In the present study, different photoperiods and nutritional conditions were applied to a mixed wastewater-borne cyanobacterial culture in order to enhance the intracellular accumulation of polyhydroxybutyrates (PHBs) and carbohydrates. Two different experimental set-ups were used. In the first, the culture was permanently exposed to illumination, while in the second it was submitted to light/dark alternation (12 h cycles). In both cases, two different nutritional regimes were also evaluated, N-limitation and P-limitation. Results showed that the highest PHB concentration (104 mg L−1) was achieved under P limited conditions and permanent illumination, whereas the highest carbohydrate concentration (838 mg L−1) was obtained under N limited condition and light/dark alternation. With regard to bioplastics and biofuel generation, this study demonstrates that the accumulation of PHBs (bioplastics) and carbohydrates (potential biofuel substrate) is favored in wastewater-borne cyanobacteria under conditions where nutrients are limited. Graphical abstract

Authors:Alessandro Presentato; Elena Piacenza; Max Anikovskiy; Martina Cappelletti; Davide Zannoni; Raymond J. TurnerPages: 1 - 8Abstract: Publication date: 25 March 2018 Source:New Biotechnology, Volume 41 Author(s): Alessandro Presentato, Elena Piacenza, Max Anikovskiy, Martina Cappelletti, Davide Zannoni, Raymond J. Turner The wide anthropogenic use of selenium compounds represents the major source of selenium pollution worldwide, causing environmental issues and health concerns. Microbe-based strategies for metal removal/recovery have received increasing interest thanks to the association of the microbial ability to detoxify toxic metal/metalloid polluted environments with the production of nanomaterials. This study investigates the tolerance and the bioconversion of selenite (SeO3 2−) by the aerobically grown Actinomycete Rhodococcus aetherivorans BCP1 in association with its ability to produce selenium nanoparticles and nanorods (SeNPs and SeNRs). The BCP1 strain showed high tolerance towards SeO3 2− with a Minimal Inhibitory Concentration (MIC) of 500mM. The bioconversion of SeO3 2− was evaluated considering two different physiological states of the BCP1 strain, i.e. unconditioned and/or conditioned cells, which correspond to cells exposed for the first time or after re-inoculation in fresh medium to either 0.5 or 2mM of Na2SeO3, respectively. SeO3 2− bioconversion was higher for conditioned grown cells compared to the unconditioned ones. Selenium nanostructures appeared polydisperse and not aggregated, as detected by electron microscopy, being embedded in an organic coating likely responsible for their stability, as suggested by the physical-chemical characterization. The production of smaller and/or larger SeNPs was influenced by the initial concentration of provided precursor, which resulted in the growth of longer and/or shorter SeNRs, respectively. The strong ability to tolerate high SeO3 2− concentrations coupled with SeNP and SeNR biosynthesis highlights promising new applications of Rhodococcus aetherivorans BCP1 as cell factory to produce stable Se-nanostructures, whose suitability might be exploited for biotechnology purposes.

Authors:Hoang-Anh T. Tu; Eleanor P. Dobson; Luke C. Henderson; Colin J. Barrow; Jacqui L. AdcockPages: 25 - 33Abstract: Publication date: 25 March 2018 Source:New Biotechnology, Volume 41 Author(s): Hoang-Anh T. Tu, Eleanor P. Dobson, Luke C. Henderson, Colin J. Barrow, Jacqui L. Adcock Specialized pro-resolving mediators are lipid signaling molecules synthesized from omega-3 and -6 polyunsaturated fatty acids, which promote the resolution of the inflammatory response. They are potential drug targets for the treatment of numerous conditions linked with uncontrolled inflammation. Many of these mediators can be effectively synthesized using enzymes, such as lipoxygenases. However, these enzymes are expensive to purchase and can be difficult to isolate. In this work, we show that commercial soy flour can be used directly as a source of lipoxygenase for the biosynthesis of specialized pro-resolving mediators from DHA and other biologically important fatty acids. The reaction was optimized and the products characterized. We found that the reaction yield and products were comparable to those synthesized using a commercial 15-lipoxygenase preparation. Graphical abstract

Authors:Imma Gifuni; Giuseppe Olivieri; Antonino Pollio; Antonio MarzocchellaPages: 46 - 54Abstract: Publication date: 25 March 2018 Source:New Biotechnology, Volume 41 Author(s): Imma Gifuni, Giuseppe Olivieri, Antonino Pollio, Antonio Marzocchella The recent trends in microalgal cultures are focused on the biorefinery of the biomass components. Some of them are not completely valorised, for example starch. Since there is a wide market for starch products in food and non-food industries, the exploitation of microalgal starch fractions could improve the economic sustainability of microalgae production. In this perspective, the optimization of nitrogen and carbon source uptake for starch accumulation is a critical point for reducing the nitrogen requirement footprint and to increase CO2 capture. In this study, four robust microalgal strains, already known as starch-accumulating strain, were investigated: Chlorella sorokiniana, Scenedesmus vacuolatus, Dunaliella tertiolecta, and Tetraselmis chuii. C. sorokiniana was selected as the best starch producer in the biorefinery context, and the role nitrogen and CO2 concentration had on the starch production was investigated. For light irradiance of 300μmolm−2 s−1 the optimal nitrogen concentration for growth and starch accumulation resulted 32mgL−1. The CO2 concentration clearly does not influence the starch accumulation, but concentrations distant from 2% negatively influence microalgal growth, affecting the final starch productivity. The biomass composition during the batch growth of C. sorokiniana was also analysed in order to explicitly characterise the dynamic of starch accumulation during the different growth phases. Protein content decreased during N-depletion, carbohydrates were mainly produced during the early N-depletion, followed by the accumulation of lipids in the late depletion.

Authors:Leonie Marang; Mark C.M. van Loosdrecht; Robbert KleerebezemPages: 55 - 61Abstract: Publication date: 25 March 2018 Source:New Biotechnology, Volume 41 Author(s): Leonie Marang, Mark C.M. van Loosdrecht, Robbert Kleerebezem To enrich polyhydroxyalkanoate (PHA) producing microbial communities, generally, a feast-famine regime is applied. Here we investigated the impact of continuous substrate feeding on the enrichment of PHA-producing bacteria in two sequencing batch reactors (SBRs). In the first reactor, the substrate (acetate) was dosed continuously and Zoogloea sp. was enriched. The culture accumulated PHA upon exposure to excess carbon, but the PHA production rate and storage capacity (53 wt.%) were one-fifth of that observed for enrichment cultures in a standard, pulse-fed SBR dominated by the PHA producer Plasticicumulans acidivorans. In the second reactor, half the acetate was dosed at the beginning of the cycle and the other half continuously. Having a true feast phase, the enrichment of P. acidivorans was not impeded by the continuous supply of acetate and the culture accumulated 85 wt.% PHA. This shows that for the enrichment of bacteria with a superior PHA-producing capacity periodic substrate excess – a true feast phase – is essential, while periodic substrate absence – a true famine phase – is not. Graphical abstract

Authors:Alfredo Aguilar; Roland Wohlgemuth; Tomasz TwardowskiPages: 1 - 4Abstract: Publication date: 25 January 2018 Source:New Biotechnology, Volume 40, Part A Author(s): Alfredo Aguilar, Roland Wohlgemuth, Tomasz Twardowski The security of food, feed and energy supply, resource efficiency and the creation of sustainable economic value and jobs for a growing population represent interlinked global challenges demanding new approaches and paradigms. One of them is bioeconomy, which ranks very high on national and international agendas, strategies and blueprints. This special issue brings together a series of unique contributions by some of the leading experts on bioeconomy with a special focus on biotechnology as the pillar of bioeconomy. The articles cover different aspects and are structured into sections on global perspectives, regional dimensions, examples of national initiatives, examples of regional and local case studies, transnational clusters and technology platforms, intellectual property rights, bio-industry associations and new scientific and technological trends in bioeconomy. A final article discussing perspectives on bioeconomy concludes this series of publications. We hope that readers will enjoy the first comprehensive insight into bioeconomy at the global level.

Authors:Yvonne Lokko; Marc Heijde; Karl Schebesta; Philippe Scholtès; Marc Van Montagu; Mauro GiaccaPages: 5 - 10Abstract: Publication date: 25 January 2018 Source:New Biotechnology, Volume 40, Part A Author(s): Yvonne Lokko, Marc Heijde, Karl Schebesta, Philippe Scholtès, Marc Van Montagu, Mauro Giacca To transform developing and least developing countries into industrialised ones, biotechnology could be deployed along the value chain, to provide support to the development of the bio-based industries in such a way to ensure sustainability of the sector and to reduce negative environmental impacts that might otherwise occur. In agribusiness development, for instance, interventions could start from inputs and agricultural mechanization, modern processing technologies, packaging of perishable products, the promotion of food safety in the processing and regulatory environment; and interventions to improve competitiveness and productivity. Worth over USD 300 billion in revenue, the role of the biotechnology goes beyond industrial growth, since it provides opportunities for progress towards many of the UN sustainable development goals (SDGs). This paper reviews the status of industrial biotechnology as it relates to inclusive and sustainable industrial development.

Authors:John Bell; Lino Paula; Thomas Dodd; Szilvia Németh; Christina Nanou; Voula Mega; Paula CamposPages: 25 - 30Abstract: Publication date: 25 January 2018 Source:New Biotechnology, Volume 40, Part A Author(s): John Bell, Lino Paula, Thomas Dodd, Szilvia Németh, Christina Nanou, Voula Mega, Paula Campos This article outlines the current context and the development of the European Bioeconomy Strategy. It analyses the current situation, challenges and needs for EU action and concludes with the next steps that the European Commission will undertake to review and update the Bioeconomy Strategy. Bioeconomy offers great opportunities to realising a competitive, circular and sustainable economy with a sound industrial base that is less dependent on fossil carbon. A sustainable bioeconomy also contributes to climate change mitigation, with oceans, forests and soils being major carbon sinks and fostering negative CO2 emissions. The EU has invested significantly in research and innovation in this field and the European Commission is committed to lead on European bioeconomy strategy.

Authors:Albert Sasson; Carlos MalpicaPages: 40 - 45Abstract: Publication date: 25 January 2018 Source:New Biotechnology, Volume 40, Part A Author(s): Albert Sasson, Carlos Malpica This article provides the authors’ view on how Latin America has embraced bioeconomy principles in the last two decades with different levels of socio-economic impact. Examples of biodiversity resource valorization in medicine, eco-intensification of agriculture, biotechnology applications in mature sectors such as mining, food and beverage production, bio-refineries and ecosystem services are provided. The importance of participatory and social innovation initiatives is highlighted.

Authors:Ruiyan Wang; Qin Cao; Qiuwei Zhao; Yin LiPages: 46 - 51Abstract: Publication date: 25 January 2018 Source:New Biotechnology, Volume 40, Part A Author(s): Ruiyan Wang, Qin Cao, Qiuwei Zhao, Yin Li With its vast population of over 1.4 billion, China is predicted soon to become the biggest single-country market in the world. The large population offers not only immense economic opportunity but also poses serious challenges related to resource depletion, pollution, and environmental degradation. To solve these burgeoning problems, biotechnology appears to be particularly well-positioned, since the Chinese government and large Chinese companies provide strong support towards the development of this field in terms both of policy and finance. Moreover, active research and commercial applications have led to rapid development of the Chinese bioindustry and bioeconomy. Chinese bioindustry is considered to be at the forefront of those of the developing and emerging countries and has added value to the country’s economy and society. This study summarizes the development and current status of Chinese bioindustry, from research and development to recent market trends. It thus can be considered as a quick-glance resource for the various stakeholders in the biotechnology sector.

Authors:Mahaletchumy Arujanan; Muthu SingaramPages: 52 - 59Abstract: Publication date: 25 January 2018 Source:New Biotechnology, Volume 40, Part A Author(s): Mahaletchumy Arujanan, Muthu Singaram Since 1990s Malaysia aspired to make biotechnology and bioeconomy as her engines of economic growth to utlise the abundance of natural resources and biodiversity. The public sector plays an integral role in developing the sector and various incentives are in place for the private sector to be actively involved and to forge collaboration with the public sector. The country launched its National Biotechnology Policy in 2005 and later launched its National Bioeconomy Programme in 2010 to become the first country in South East Asia and second in Asia after China to have such an initiative. Malaysia is also very proactive in its biosafety law and regulations and has most of the related legal instrument in place. A lot of success has been recorded since the inception of the National Biotechnology Policy in terms of job creation, contribution to GDP through biobusinesses and investment from foreign companies, but the sector is not spared from challenges too. Due to the nature of the discipline that is multidisciplinary and that requires huge amount of investment, expertise and political will, there are a lot of barriers before the country emerges as a bioeconomy player. This paper discusses the public policies, initiatives and funding mechanisms in place in Malaysia that drive its research, development and commercialisation in the area of biotechnology and bioeconomy. The authors also discuss the challenges faced in Malaysia in implementing the policies.

Authors:Venkata Mohan S.; Chiranjeevi P.; Shikha Dahiya; Naresh Kumar A.Pages: 60 - 69Abstract: Publication date: 25 January 2018 Source:New Biotechnology, Volume 40, Part A Author(s): Venkata Mohan S., Chiranjeevi P., Shikha Dahiya, Naresh Kumar A. Environmental and climatic change issues, population explosion, rapid urbanisation, depletion of fossil reserves, need for energy security, huge waste generation, etc. are some of the inherent issues associated with the fossil based linear economy which need greater attention. In this context, the world is gradually transforming from fossil-based economy to a sustainable circular bio-economy. The biogenic waste which is generated in enormous quanties in India can be considered as potential feedstock for structuring the bio-based economy. This communication depicts the need for developing waste derived bioeconomy in the Indian perspective. Waste is now being perceived as a resource with value and believed to supplement petroleum feedstock to a great extent if properly utilized. The necessity to introduce waste as the core element for the future economic models which also allows sustainable development is discussed. The review also establishes drivers for the bioeconomy and structures the waste derived bioeconomy in a sustainable format to address the futuristic needs, scope and opportunities envisaged in the business and economic realm. The enabling technologies/processes that can be applied for biogenic wastes valorisation are elaborated. Circularizing the economy in a waste biorefinery model for the production of biobased products including bioenergy is discussed.

Authors:Alicia Paz; David Outeiriño; Ricardo Pinheiro de Souza Oliveira; José Manuel DomínguezPages: 186 - 191Abstract: Publication date: 25 January 2018 Source:New Biotechnology, Volume 40, Part B Author(s): Alicia Paz, David Outeiriño, Ricardo Pinheiro de Souza Oliveira, José Manuel Domínguez Bacillus aryabhattai BA03, a strain isolated in our laboratory, has interesting properties related to the production of natural aromas and flavors. Specifically, we have found that it was able to produce vanillin from ferulic acid (FA). Furthermore, this strain produces high amounts of 4-vinylguaiacol in only 14h, this being the only intermediate metabolite observed in the process. FA is an inexpensive feedstock for the production of natural value-added compounds when extracted from lignocellulosic wastes. In this study, we optimized the operational conditions (temperature, pH and agitation), medium composition and bioconversion technology (batch or fed-batch) to produce vanillin. In a fed-batch process conducted with just one additional supplementation after 24h, the maximal concentration of vanillin (147.1±0.9mg/L) was observed after 216h (QV =0.681mg/Lh; YV/fFA =0.082mg/mg) after degrading 90.3% FA. In view of our data, we postulate that Bacillus aryabhattai BA03 carries out a decarboxylation of ferulic acid as a metabolic pathway. Graphical abstract

Authors:Rubén Vicente; Rafael Martínez-Carrasco; Pilar Pérez; Rosa MorcuendePages: 192 - 199Abstract: Publication date: 25 January 2018 Source:New Biotechnology, Volume 40, Part B Author(s): Rubén Vicente, Rafael Martínez-Carrasco, Pilar Pérez, Rosa Morcuende The use of correlation networks and hierarchical cluster analysis provides a framework to organize and study the coordination of parameters such as genes, metabolites, proteins and physiological parameters. We have analyzed 142 traits from primary C and N metabolism, including biochemical and gene expression analyses, in a range of 32 different growth conditions (various [CO2] levels, temperatures, N supplies, growth stages and experimental methods). To test the integration of primary metabolism, particularly under climate change, we investigated which C and N metabolic traits and transcript levels are correlated in durum wheat flag leaves using a correlation network and a hierarchical cluster analysis. There was a high amount of positive correlation between traits involved in a wide range of biological processes, suggesting a close and intricate coordination between C-N metabolisms at the biochemical and transcriptional levels. Transcript levels for genes related to N uptake and assimilation were especially coexpressed with genes belonging to the respiratory pathway, highlighting the coordination between the synthesis of organic N compounds and provision of energy and C skeletons. Also involved in this coordination were Rubisco and nitrate reductase activities, which play a key role in the regulation of plant metabolism. Carbohydrate accumulation was linked with a down-regulation of photosynthetic and N metabolism genes and nitrate reductase activity. Based on the degree of connectivity between nodes, network exploration facilitated the identification of some traits that may be biologically relevant during plant abiotic stress tolerance, as most of them are involved in limiting steps of plant metabolism. Graphical abstract

Authors:Gilda Carvalho; Inês Pedras; Soren M. Karst; Catarina S.S. Oliveira; Anouk F. Duque; Per H. Nielsen; Maria A.M. ReisPages: 207 - 217Abstract: Publication date: 25 January 2018 Source:New Biotechnology, Volume 40, Part B Author(s): Gilda Carvalho, Inês Pedras, Soren M. Karst, Catarina S.S. Oliveira, Anouk F. Duque, Per H. Nielsen, Maria A.M. Reis Polyhydroxyalkanoates (PHA) are biopolymers that can be produced by mixed microbial cultures using wastes or industrial by-products, which represent an economical and environmental advantage over pure culture processes. The use of alternate feedstocks enables using seasonal by-products, providing that the process is resilient to transient conditions. The mixed microbial communities of a 3-stage PHA producing system fed initially with molasses and then cheese whey were investigated through amplicon sequencing of the 16S rRNA gene. The transition in feedstock resulted in an adaptation of the acidogenic community, where Actinobacteria dominated with sugarcane molasses (up to 93% of the operational taxonomic units) and Firmicutes, with cheese whey (up to 97%). The resulting fermentation products profile also changed, with a higher fraction of HV precursors obtained with molasses than cheese whey (7.1±0.5 and 1.7±0.7 gCOD/L, respectively). As for the PHA storing culture, the genera Azoarcus, Thauera and Paracoccus were enriched with fermented molasses (average 89% of Bacteria). Later, fermented cheese whey fostered a higher diversity, including some less characterised PHA-storers such as the genera Paenibacillus and Lysinibacillus. Although the microbial community structure was significantly affected by the feedstock shift, the acidogenic and PHA storing performance of the 3-stage system was very similar once a pseudo steady state was attained, showing that a reliable level of functional redundancy was attained in both mixed cultures.

Authors:Renata N. Florindo; Valquiria P. Souza; Hemily S. Mutti; Cesar Camilo; Lívia Regina Manzine; Sandro R. Marana; Igor Polikarpov; Alessandro S. NascimentoPages: 218 - 227Abstract: Publication date: 25 January 2018 Source:New Biotechnology, Volume 40, Part B Author(s): Renata N. Florindo, Valquiria P. Souza, Hemily S. Mutti, Cesar Camilo, Lívia Regina Manzine, Sandro R. Marana, Igor Polikarpov, Alessandro S. Nascimento β-glucosidases are glycoside hydrolases able to cleave small and soluble substrates, thus producing monosaccharides. These enzymes are distributed among families GH1, GH2, GH3, GH5, GH9, GH30 and GH116, with GH1 and GH3 being the most relevant families with characterized enzymes to date. A recent transcriptomic analysis of the fungus Trichoderma harzianum, known for its increased β-glucosidase activity as compared to Trichoderma reesei, revealed two enzymes from family GH1 with high expression levels. Here we report the cloning, recombinant expression, purification and crystallization of these enzymes, ThBgl1 and ThBgl2. A close inspection of the enzymatic activity of these enzymes surprisingly revealed a marked difference between them despite the sequence similarity (53%). ThBgl1 has an increased tendency to catalyze transglycosylation reaction while ThBgl2 acts more as a hydrolyzing enzyme. Detailed comparison of their crystal structures and the analysis of the molecular dynamics simulations reveal the presence of an asparagine residue N186 in ThBgl2, which is replaced by the phenylalanine F180 in ThBgl1. This single amino acid substitution seems to be sufficient to create a polar environment that culminates with an increased availability of water molecules in ThBgl2 as compared to ThBgl1, thus conferring stronger hydrolyzing character to the former enzyme.

Authors:Daniel Foshag; Erik Henrich; Ekkehard Hiller; Miriam Schäfer; Christian Kerger; Anke Burger-Kentischer; Irene Diaz-Moreno; Sofía M. García-Mauriño; Volker Dötsch; Steffen Rupp; Frank BernhardPages: 245 - 260Abstract: Publication date: 25 January 2018 Source:New Biotechnology, Volume 40, Part B Author(s): Daniel Foshag, Erik Henrich, Ekkehard Hiller, Miriam Schäfer, Christian Kerger, Anke Burger-Kentischer, Irene Diaz-Moreno, Sofía M. García-Mauriño, Volker Dötsch, Steffen Rupp, Frank Bernhard Protein production using processed cell lysates is a core technology in synthetic biology and these systems are excellent to produce difficult toxins or membrane proteins. However, the composition of the central lysate of cell-free systems is still a “black box”. Escherichia coli lysates are most productive for cell-free expression, yielding several mgs of protein per ml of reaction. Their preparation implies proteome fractionation, resulting in strongly biased and yet unknown lysate compositions. Many metabolic pathways are expected to be truncated or completely removed. The lack of knowledge of basic cell-free lysate proteomes is a major bottleneck for directed lysate engineering approaches as well as for assay design using non-purified reaction mixtures. This study is starting to close this gap by providing a blueprint of the S30 lysate proteome derived from the commonly used E. coli strain A19. S30 lysates are frequently used for cell-free protein production and represent the basis of most commercial E. coli cell-free expression systems. A fraction of 821 proteins was identified as the core proteome in S30 lysates, representing approximately a quarter of the known E. coli proteome. Its classification into functional groups relevant for transcription/translation, folding, stability and metabolic processes will build the framework for tailored cell-free reactions. As an example, we show that SOS response induction during cultivation results in tuned S30 lysate with better folding capacity, and improved solubility and activity of synthesized proteins. The presented data and protocols can serve as a platform for the generation of customized cell-free systems and product analysis. Graphical abstract

Authors:Kristine Rose M. Ramos; Kris Niño G. Valdehuesa; Grace M. Nisola; Won-Keun Lee; Wook-Jin ChungPages: 261 - 267Abstract: Publication date: 25 January 2018 Source:New Biotechnology, Volume 40, Part B Author(s): Kristine Rose M. Ramos, Kris Niño G. Valdehuesa, Grace M. Nisola, Won-Keun Lee, Wook-Jin Chung Research on the enzymatic breakdown of seaweed-derived agar has recently gained attention due to the progress in green technologies for marine biomass utilization. The enzymes known as agarases catalyze the cleavage of glycosidic bonds within the polysaccharide. In this study, a new β-agarase, Aga2, was identified from Cellulophaga omnivescoria W5C. Aga2 is one of four putative agarases from the W5C genome, and it belongs to the glycoside hydrolase 16 family. It was shown to be exclusive to the Cellulophaga genus. Agarase activity assays showed that Aga2 is an endolytic-type β-agarase that produces tetrameric and hexameric neoagaro-oligosaccharides, with optimum activity at 45°C and pH 8.0. Zinc ions slightly enhanced its activity while manganese ions had inhibitory effects even at very low concentrations. Aga2 has a Km of 2.59mgmL−1 and Vmax of 275.48Umg−1. The Kcat is 1.73×102 s−1, while the Kcat/Km is 8.04×106 s−1 M−1. Aga2 also showed good thermostability at 45°C and above, and retained >90% of its activity after repeated freeze-thaw cycles. Bioinformatic analysis of its amino acid sequence revealed that intrinsic properties of the protein (e.g. presence of certain dipeptides and the relative volume occupied by aliphatic amino acids) and tertiary structural elements (e.g. presence of salt bridges, hydrophobic interactions and H-bonding) contributed to its thermostability.